This is a list of Pokémon in the order dictated by the New Pokédex introduced in Generation II, putting the Johto starter Pokémon first, and following them with Pokémon native to both Kanto and Johto in a different order, according to their evolution.

Because many of the Pokémon native to Johto are also native to Kanto, for the most part, this is merely a reordered Pokédex list to place related Pokémon closer to their evolutionary kin. For example, in this scheme, Pichu comes directly before Pikachu and Raichu, and Scyther comes directly before Scizor.

Interestingly, the order was never referred to directly as the "Johto Pokédex" in-game in Generation II, instead being called the "New Pokédex", where the National order was referred to as the "Old Pokédex". This discrepancy was validated in the Generation IV remakes (which explicitly refer to their ordering system as the Johto Pokédex), with several Pokémon not in the same order, to allow for the inclusion of the five Pokémon that evolve from Generation I and Generation II Pokémon by learning a move (i.e. Lickilicky, Mamoswine, Tangrowth, Yanmega, and Ambipom) as they learn their evolution-activating moves automatically. This new order can be found at List of Pokémon by Johto Pokédex number. Up to #101 (Yanma), Generation II's New Pokédex and Generation IV's Johto Pokédex have the same order; however, the two diverge at #102, which is given to Sunkern in Generation II's New Pokédex and Yanmega in Generation IV's Johto Pokédex.